Re: [Rdkit-discuss] Documentation as pdf
On Fri, May 29, 2020 at 8:15 AM Eduardo Mayo wrote: > Please is any documentation for the 2020.3 available as a PDF or any > format that work offline?? > I stopped producing the PDFs of the documentation because it ends up being tricky to do so and the resulting docs don't look very good. If you want an offline version, the easiest thing to do is just download the HTML doc package and extract it locally: https://rdkit.org/RDKit_Docs.current.tgz (I had forgotten to update that link when I did the last release, but that's now fixed) Best, -greg > ___ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
[Rdkit-discuss] Documentation as pdf
Please is any documentation for the 2020.3 available as a PDF or any format that work offline?? ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Documentation Update
It is slightly annoying that a google search rdkit fav_rdkit_method now returns dead 404 links e.g. search for rdkit MolFromSmiles, returns http://www.rdkit.org/Python_Docs/rdkit.Chem.rdmolfiles-module.html as the first link (404 file not found). This is no doubt because of moving the docs to another location - can you maybe URL alias so that these top search results links are not broken? If not, this is no big deal -- if it is not worth your time we just need to wait till the google crawler visits the rdkit site again. - Jean-Paul Ebejer Early Stage Researcher On 8 January 2012 05:12, Greg Landrum greg.land...@gmail.com wrote: Dear all, The online version of the documentation has been updated for the new release: http://www.rdkit.org/docs/index.html This includes links to the API documentation for both Python and C++. The package can be downloaded if you want a local copy: http://www.rdkit.org/RDKit_Docs.2011_12_1.tgz And there's a PDF of the non-API pieces of the docs (i.e. the Getting Started in Python and RDKit Books sections): http://www.rdkit.org/RDKit_Docs.2011_12_1.pdf Please let me know if you have feedback or suggestions for the new documentation, -greg -- Ridiculously easy VDI. With Citrix VDI-in-a-Box, you don't need a complex infrastructure or vast IT resources to deliver seamless, secure access to virtual desktops. With this all-in-one solution, easily deploy virtual desktops for less than the cost of PCs and save 60% on VDI infrastructure costs. Try it free! http://p.sf.net/sfu/Citrix-VDIinabox ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss -- Ridiculously easy VDI. With Citrix VDI-in-a-Box, you don't need a complex infrastructure or vast IT resources to deliver seamless, secure access to virtual desktops. With this all-in-one solution, easily deploy virtual desktops for less than the cost of PCs and save 60% on VDI infrastructure costs. Try it free! http://p.sf.net/sfu/Citrix-VDIinabox___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Documentation Update
On Mon, Jan 9, 2012 at 10:45 AM, JP jeanpaul.ebe...@inhibox.com wrote: It is slightly annoying that a google search rdkit fav_rdkit_method now returns dead 404 links e.g. search for rdkit MolFromSmiles, returns http://www.rdkit.org/Python_Docs/rdkit.Chem.rdmolfiles-module.html as the first link (404 file not found). damn! I thought I had include symlinks so that old urls would work. I can't fix this now, but I will take care of it when I get home tonight. Sorry about that. -greg -- Ridiculously easy VDI. With Citrix VDI-in-a-Box, you don't need a complex infrastructure or vast IT resources to deliver seamless, secure access to virtual desktops. With this all-in-one solution, easily deploy virtual desktops for less than the cost of PCs and save 60% on VDI infrastructure costs. Try it free! http://p.sf.net/sfu/Citrix-VDIinabox ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
[Rdkit-discuss] Documentation Update
Dear all, The online version of the documentation has been updated for the new release: http://www.rdkit.org/docs/index.html This includes links to the API documentation for both Python and C++. The package can be downloaded if you want a local copy: http://www.rdkit.org/RDKit_Docs.2011_12_1.tgz And there's a PDF of the non-API pieces of the docs (i.e. the Getting Started in Python and RDKit Books sections): http://www.rdkit.org/RDKit_Docs.2011_12_1.pdf Please let me know if you have feedback or suggestions for the new documentation, -greg -- Ridiculously easy VDI. With Citrix VDI-in-a-Box, you don't need a complex infrastructure or vast IT resources to deliver seamless, secure access to virtual desktops. With this all-in-one solution, easily deploy virtual desktops for less than the cost of PCs and save 60% on VDI infrastructure costs. Try it free! http://p.sf.net/sfu/Citrix-VDIinabox ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
[Rdkit-discuss] Documentation example doesn't work... section 3.5
Copying the example verbatim from the documentation (section 3.5 working
with 3d molecules) doesn't work:
from rdkit import Chem
from rdkit.Chem import AllChem
m = Chem.MolFromSmiles('C1CCC1OC')
m2 = Chem.AddHs(m)
m
rdkit.Chem.rdchem.Mol object at 0x1f02bb0
m2
rdkit.Chem.rdchem.Mol object at 0x1f021a0
AllChem.UFFOptimizeMolecule(m2)
Traceback (most recent call last):
File stdin, line 1, in module
ValueError: Bad Conformer Id
Any ideas why?
from rdkit import rdBase
rdBase._version()
'$Id: RDBase.cpp 1528 2010-09-26 17:04:37Z glandrum $'
Cheers
JP
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Re: [Rdkit-discuss] Documentation example doesn't work... section 3.5
Hi JP:
On Tue, Apr 12, 2011 at 5:35 AM, JP jeanpaul.ebe...@inhibox.com wrote:
Copying the example verbatim from the documentation (section 3.5 working
with 3d molecules) doesn't work:
from rdkit import Chem
from rdkit.Chem import AllChem
m = Chem.MolFromSmiles('C1CCC1OC')
m2 = Chem.AddHs(m)
m
rdkit.Chem.rdchem.Mol object at 0x1f02bb0
m2
rdkit.Chem.rdchem.Mol object at 0x1f021a0
AllChem.UFFOptimizeMolecule(m2)
Traceback (most recent call last):
File stdin, line 1, in module
ValueError: Bad Conformer Id
Any ideas why?
You forgot one step, before optimizing the molecule you need to add 3D
coordinates:
AllChem.EmbedMolecule(m2)
0
-greg
--
Forrester Wave Report - Recovery time is now measured in hours and minutes
not days. Key insights are discussed in the 2010 Forrester Wave Report as
part of an in-depth evaluation of disaster recovery service providers.
Forrester found the best-in-class provider in terms of services and vision.
Read this report now! http://p.sf.net/sfu/ibm-webcastpromo
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Re: [Rdkit-discuss] Documentation example doesn't work... section 3.5
DOH!!!
Apologies...
On 12 April 2011 11:02, Greg Landrum greg.land...@gmail.com wrote:
Hi JP:
On Tue, Apr 12, 2011 at 5:35 AM, JP jeanpaul.ebe...@inhibox.com wrote:
Copying the example verbatim from the documentation (section 3.5 working
with 3d molecules) doesn't work:
from rdkit import Chem
from rdkit.Chem import AllChem
m = Chem.MolFromSmiles('C1CCC1OC')
m2 = Chem.AddHs(m)
m
rdkit.Chem.rdchem.Mol object at 0x1f02bb0
m2
rdkit.Chem.rdchem.Mol object at 0x1f021a0
AllChem.UFFOptimizeMolecule(m2)
Traceback (most recent call last):
File stdin, line 1, in module
ValueError: Bad Conformer Id
Any ideas why?
You forgot one step, before optimizing the molecule you need to add 3D
coordinates:
AllChem.EmbedMolecule(m2)
0
-greg
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Re: [Rdkit-discuss] Documentation link not working
On Thu, Feb 3, 2011 at 8:48 PM, Greg Landrum greg.land...@gmail.com wrote: Dear JP, On Thu, Feb 3, 2011 at 4:09 PM, JP jeanpaul.ebe...@inhibox.com wrote: The link to: http://rdkit.svn.sourceforge.net/viewvc/*checkout*/rdkit/trunk/Docs/Book/GettingStartedInPython.pdf On the wiki page: http://code.google.com/p/rdkit/wiki/GettingStarted Is broken!! Can't access my fav pdf :) viewvc at sourceforge is down at the moment. You can get the file directly here: http://rdkit.svn.sourceforge.net/svnroot/rdkit/trunk/Docs/RDKit_Overview.pdf apologies, the correct link is: http://rdkit.svn.sourceforge.net/svnroot/rdkit/trunk/Docs/Book/GettingStartedInPython.pdf -greg -- The modern datacenter depends on network connectivity to access resources and provide services. The best practices for maximizing a physical server's connectivity to a physical network are well understood - see how these rules translate into the virtual world? http://p.sf.net/sfu/oracle-sfdevnlfb ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
[Rdkit-discuss] Documentation
Dear Greg, I successfully installed RDKit_Q12010_1. I have been pleased to see that the 2D coordinate generation algorithm is now able to deal with all structures in my test structure file. I was able to generate the C++ documentation using doxygen. How do you generate the python documentation? I read something about HappyDoc in RDKit_Overview.pdf. I tried to install HappyDoc but no setup.py file for its installation. Maybe a few lines about documentation generation could be added in the INSTALL file of the RDKit. Best regards, Jean-Marc Nuzillard -- ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Documentation
Hi Jean-Marc, On Mon, May 3, 2010 at 1:49 PM, JEAN MARC NUZILLARD jm.nuzill...@univ-reims.fr wrote: Dear Greg, I successfully installed RDKit_Q12010_1. I have been pleased to see that the 2D coordinate generation algorithm is now able to deal with all structures in my test structure file. glad to hear it. I was able to generate the C++ documentation using doxygen. How do you generate the python documentation? I read something about HappyDoc in RDKit_Overview.pdf. I tried to install HappyDoc but no setup.py file for its installation. To build the python documentation you need to install epydoc: http://epydoc.sourceforge.net/ once you have the install completed, you build the documentation as follows: cd $RDBASE/rdkit epydoc --config epydoc.config -o ../Docs/Code/Python there will be some errors displayed; you can safely ignore them. Maybe a few lines about documentation generation could be added in the INSTALL file of the RDKit. good idea, I will update the wiki and the INSTALL file. Thanks for the suggestion, -greg -- ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
